Job ID = 6366597 SRX = SRX208766 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:54:11 prefetch.2.10.7: 1) Downloading 'SRR628900'... 2020-06-15T22:54:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:55:25 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:55:26 prefetch.2.10.7: 'SRR628900' is valid 2020-06-15T22:55:26 prefetch.2.10.7: 1) 'SRR628900' was downloaded successfully Read 13809537 spots for SRR628900/SRR628900.sra Written 13809537 spots for SRR628900/SRR628900.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:33 13809537 reads; of these: 13809537 (100.00%) were unpaired; of these: 4713549 (34.13%) aligned 0 times 7953965 (57.60%) aligned exactly 1 time 1142023 (8.27%) aligned >1 times 65.87% overall alignment rate Time searching: 00:03:33 Overall time: 00:03:33 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 2016910 / 9095988 = 0.2217 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:02:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX208766/SRX208766.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX208766/SRX208766.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX208766/SRX208766.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX208766/SRX208766.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 08:02:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:03:02: 1000000 INFO @ Tue, 16 Jun 2020 08:03:10: 2000000 INFO @ Tue, 16 Jun 2020 08:03:18: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:03:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX208766/SRX208766.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX208766/SRX208766.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX208766/SRX208766.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX208766/SRX208766.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 08:03:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:03:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:03:26: 4000000 INFO @ Tue, 16 Jun 2020 08:03:33: 1000000 INFO @ Tue, 16 Jun 2020 08:03:35: 5000000 INFO @ Tue, 16 Jun 2020 08:03:41: 2000000 INFO @ Tue, 16 Jun 2020 08:03:44: 6000000 INFO @ Tue, 16 Jun 2020 08:03:49: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:03:52: 7000000 INFO @ Tue, 16 Jun 2020 08:03:53: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:03:53: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:03:53: #1 total tags in treatment: 7079078 INFO @ Tue, 16 Jun 2020 08:03:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:03:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:03:53: #1 tags after filtering in treatment: 7079078 INFO @ Tue, 16 Jun 2020 08:03:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:03:53: #1 finished! INFO @ Tue, 16 Jun 2020 08:03:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:03:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:03:54: #2 number of paired peaks: 123 WARNING @ Tue, 16 Jun 2020 08:03:54: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Tue, 16 Jun 2020 08:03:54: start model_add_line... INFO @ Tue, 16 Jun 2020 08:03:54: start X-correlation... INFO @ Tue, 16 Jun 2020 08:03:54: end of X-cor INFO @ Tue, 16 Jun 2020 08:03:54: #2 finished! INFO @ Tue, 16 Jun 2020 08:03:54: #2 predicted fragment length is 61 bps INFO @ Tue, 16 Jun 2020 08:03:54: #2 alternative fragment length(s) may be 3,61 bps INFO @ Tue, 16 Jun 2020 08:03:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX208766/SRX208766.05_model.r WARNING @ Tue, 16 Jun 2020 08:03:54: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:03:54: #2 You may need to consider one of the other alternative d(s): 3,61 WARNING @ Tue, 16 Jun 2020 08:03:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:03:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:03:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:03:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX208766/SRX208766.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX208766/SRX208766.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX208766/SRX208766.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX208766/SRX208766.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 08:03:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:03:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:03:56: 4000000 INFO @ Tue, 16 Jun 2020 08:04:02: 1000000 INFO @ Tue, 16 Jun 2020 08:04:04: 5000000 INFO @ Tue, 16 Jun 2020 08:04:09: 2000000 INFO @ Tue, 16 Jun 2020 08:04:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:04:11: 6000000 INFO @ Tue, 16 Jun 2020 08:04:17: 3000000 INFO @ Tue, 16 Jun 2020 08:04:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX208766/SRX208766.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:04:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX208766/SRX208766.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:04:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX208766/SRX208766.05_summits.bed INFO @ Tue, 16 Jun 2020 08:04:17: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (201 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:04:19: 7000000 INFO @ Tue, 16 Jun 2020 08:04:19: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:04:19: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:04:19: #1 total tags in treatment: 7079078 INFO @ Tue, 16 Jun 2020 08:04:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:04:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:04:19: #1 tags after filtering in treatment: 7079078 INFO @ Tue, 16 Jun 2020 08:04:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:04:19: #1 finished! INFO @ Tue, 16 Jun 2020 08:04:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:04:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:04:20: #2 number of paired peaks: 123 WARNING @ Tue, 16 Jun 2020 08:04:20: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Tue, 16 Jun 2020 08:04:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:04:20: start X-correlation... INFO @ Tue, 16 Jun 2020 08:04:20: end of X-cor INFO @ Tue, 16 Jun 2020 08:04:20: #2 finished! INFO @ Tue, 16 Jun 2020 08:04:20: #2 predicted fragment length is 61 bps INFO @ Tue, 16 Jun 2020 08:04:20: #2 alternative fragment length(s) may be 3,61 bps INFO @ Tue, 16 Jun 2020 08:04:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX208766/SRX208766.10_model.r WARNING @ Tue, 16 Jun 2020 08:04:20: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:04:20: #2 You may need to consider one of the other alternative d(s): 3,61 WARNING @ Tue, 16 Jun 2020 08:04:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:04:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:04:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:04:24: 4000000 INFO @ Tue, 16 Jun 2020 08:04:31: 5000000 INFO @ Tue, 16 Jun 2020 08:04:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:04:38: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:04:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX208766/SRX208766.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:04:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX208766/SRX208766.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:04:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX208766/SRX208766.10_summits.bed INFO @ Tue, 16 Jun 2020 08:04:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (96 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:04:45: 7000000 INFO @ Tue, 16 Jun 2020 08:04:45: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:04:45: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:04:45: #1 total tags in treatment: 7079078 INFO @ Tue, 16 Jun 2020 08:04:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:04:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:04:45: #1 tags after filtering in treatment: 7079078 INFO @ Tue, 16 Jun 2020 08:04:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:04:45: #1 finished! INFO @ Tue, 16 Jun 2020 08:04:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:04:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:04:46: #2 number of paired peaks: 123 WARNING @ Tue, 16 Jun 2020 08:04:46: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Tue, 16 Jun 2020 08:04:46: start model_add_line... INFO @ Tue, 16 Jun 2020 08:04:46: start X-correlation... INFO @ Tue, 16 Jun 2020 08:04:46: end of X-cor INFO @ Tue, 16 Jun 2020 08:04:46: #2 finished! INFO @ Tue, 16 Jun 2020 08:04:46: #2 predicted fragment length is 61 bps INFO @ Tue, 16 Jun 2020 08:04:46: #2 alternative fragment length(s) may be 3,61 bps INFO @ Tue, 16 Jun 2020 08:04:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX208766/SRX208766.20_model.r WARNING @ Tue, 16 Jun 2020 08:04:46: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:04:46: #2 You may need to consider one of the other alternative d(s): 3,61 WARNING @ Tue, 16 Jun 2020 08:04:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:04:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:04:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:05:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:05:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX208766/SRX208766.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:05:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX208766/SRX208766.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:05:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX208766/SRX208766.20_summits.bed INFO @ Tue, 16 Jun 2020 08:05:10: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (18 records, 4 fields): 2 millis CompletedMACS2peakCalling